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Coexpression cluster:C3017: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3017_CD14_CD14CD16_Eosinophils_Mast_Neutrophils_Basophils_CD34
|id=C3017
}}

Latest revision as of 12:17, 17 September 2013


Full id: C3017_CD14_CD14CD16_Eosinophils_Mast_Neutrophils_Basophils_CD34



Phase1 CAGE Peaks

Hg19::chr10:43633941..43633960,+p3@CSGALNACT2
Hg19::chr10:43633962..43633969,+p5@CSGALNACT2
Hg19::chr10:43633970..43633986,+p4@CSGALNACT2


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
leukocyte1.71e-36136
myeloid leukocyte7.63e-3672
granulocyte monocyte progenitor cell1.29e-3267
hematopoietic lineage restricted progenitor cell1.59e-31120
myeloid lineage restricted progenitor cell2.43e-3166
defensive cell3.05e-3048
phagocyte3.05e-3048
macrophage dendritic cell progenitor4.15e-3061
nongranular leukocyte2.87e-29115
monopoietic cell5.29e-2959
monocyte5.29e-2959
monoblast5.29e-2959
promonocyte5.29e-2959
classical monocyte6.97e-2842
CD14-positive, CD16-negative classical monocyte6.97e-2842
hematopoietic stem cell1.42e-25168
angioblastic mesenchymal cell1.42e-25168
hematopoietic cell1.52e-24177
hematopoietic oligopotent progenitor cell4.06e-23161
hematopoietic multipotent progenitor cell4.06e-23161
mesenchymal cell1.29e-20354
connective tissue cell6.71e-20361
myeloid cell6.72e-20108
common myeloid progenitor6.72e-20108
motile cell9.45e-17386
multi fate stem cell1.31e-16427
somatic stem cell4.67e-16433
stem cell1.76e-15441
stuff accumulating cell8.57e-1287
mature alpha-beta T cell1.29e-0818
alpha-beta T cell1.29e-0818
immature T cell1.29e-0818
mature T cell1.29e-0818
immature alpha-beta T cell1.29e-0818
T cell2.23e-0725
pro-T cell2.23e-0725
intermediate monocyte3.01e-079
CD14-positive, CD16-positive monocyte3.01e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.33e-3698
blood island6.33e-3698
bone marrow1.60e-3076
hemolymphoid system3.91e-30108
bone element8.79e-3082
skeletal element1.10e-2890
skeletal system1.63e-27100
immune system4.68e-2593
connective tissue1.72e-19371
musculoskeletal system2.90e-15167
lateral plate mesoderm1.93e-09203


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.19.41405
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.14.7105
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.12.67616
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
MA0074.10.935474
MA0076.12.91768
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.16.20416
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.12.7096
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0189050703654271
E2F1#186934.907389214879320.008460985347239390.0323387684786948
E2F4#1874312.66806031528440.0004917987006298980.00435094997840627
E2F6#187635.017155731697390.00791769806886330.0320224787442983
EGR1#195834.988179094810140.008056488137383440.0318921868089372
ELF1#199734.258097958807540.01295179875054610.0459811309303244
ETS1#211339.728760922202340.001085840092584840.0075946995331816
FOS#235338.99795530889440.001372499272417130.00894492677141794
GABPB1#255337.067683836182170.002832212825417420.0153611069419282
HMGN3#932438.178547723350590.001827766942164210.0108257330954851
IRF1#365937.63716375356390.002244692747297240.0127562012098692
NFKB1#479035.488063424193840.006049381815655430.0268447583363177
PAX5#507936.669565531177830.003370290999677260.0172197946145146
SIN3A#2594235.408884726815140.006318961977991520.0275275744564719
TCF7L2#6934310.77017656313730.0008003181298398380.00611488954293239
THAP1#55145331.36914460285133.23800758564397e-050.00064487847871295
YY1#752834.911170749853860.008441455341808260.0327775273987104
ZBTB7A#5134137.35190930787590.002516255860282270.0139569411966658
ZNF263#1012738.221841637010680.001799043925565870.0108890378755244



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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